No abstract

Summary1. Species identification via DNA barcodes has recently become an important and routine task in many biodiversity projects using DNA sequence data. 2. Here, we present BarcodingR, an integrated software package that provides a comprehensive implementation of species identification methods, including artificial intelligence, fuzzy-set, Bayesian and kmer-based methods, that are not readily available in other packages. 3. BarcodingR additionally provides new functions for barcode evaluation, barcoding gap analysis, delimitation comparison analysis, species membership analysis and consensus identification. 4. Comparison with other barcoding methods using 11 empirical data sets indicates that on average, FZKMER (implemented in BarcodingR) and one extant barcoding method BRONX outperform all other methods examined in this study. Two other methods, BP and FZ (both implemented in BarcodingR), present similar performance as SVM and BLOG, respectively, and all display better performance than that of Jrip. 5. The software of BarcodingR is open source under GNU General Public License and freely available for all major operating systems.

Purpose The application of excessive chemical fertilizers during the cultivation of Astragalus membranaceus leads to a decline in the quality of this medicinal plant as well as the soil’s sustainable productivity. In this study, we developed a special microbial organic fertilizer for A. membranaceus and investigated its effects on plant growth and rhizosphere microbial communities. Methods The root biomass and main active components of A. membranaceus in different growth stages were measured to assess the impacts of microbial organic manure on plant growth. Meanwhile, 16S rRNA and ITS1 amplicons were amplified and high-throughput sequencing was performed to detect the dynamic impacts of microbial organic manure on rhizosphere microbial communities. Result The results demonstrated that microbial organic manure significantly increased wet and dry weights of A. membranaceus seedlings and the accumulation of two effective components (flavonoids and saponin) in bacterial fertilizer treatment groups are significant higher than the control group. Research on rhizosphere microbial flora shows that the number and polymorphism of bacteria and fungi were decreased after the application of special fertilizer during the rapid growth period of plant and then gradually increased with seedling growth. The community structure of bacteria was regulated after the application of special fertilizer, and the beneficial bacteria for plant growth are enriched. Functional profiles prediction showed that significant shifts in metabolic functions impacting KEGG pathways of the microbial fertilizer treatment groups are related to metabolism and biosynthesis. Conclusion The results indicate that the microbial organic manure can improve A. membranaceus growth by providing appropriate nutrients and regulating the rhizosphere microbial community which has good potential in ecological cultivation of A. membranaceus.

Rapid and accurate identification of species is required for the biological control of pest Noctuoidea moths. DNA barcodes and thin-film biosensor chips are two molecular approaches that have gained wide attention. Here, we compare these two methods for the identification of a limited number of Noctuoidea moth species. Based on the commonly used mitochondrial gene cytochrome c oxidase I (the standard DNA barcode for animal species), 14 probes were designed and synthesized for 14 species shared by two national nature reserves in Beijing and Hebei, China. Probes ranged in length from 18 to 27 bp and were designed as mismatch probes to guarantee that there were at least three base differences between the probe and nontarget sequences. The results on the chip could be detected by the naked eye without needing special equipment. No cross-hybridizations were detected although we tested all probes on the 14 target and 24 nontarget Noctuoidea species. The neighbour-joining tree of the 38 species based on COI sequences gave 38 highly supported independent groups. Both DNA barcoding and thin-film biosensor chips, based on the COI gene, are able to accurately identify and discriminate the 14 targeted moth species in this study. Because of its speed, high accuracy and low cost, the thin-film biosensor chip is a very practical means of species identification. Now, a more comprehensive chip will be developed for the identification of additional Noctuoidea moths for pest control and ecological protection.

Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi‐State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.